Rob this is Timsfordtruck, sounds fishy to me! I have a 2003 F250. I to have the same issue with tow/haul as you. My issue started as yours did, I lost my alternator and batteries suddenly with no warning. I have drove the truck over 600 miles this weekend. No issue with transmission at all!! But all I have to do is engage tow/haul and the light will start blinking!! I have the same codes as you and DREAD the visit to the shop to see what they will "try" until they find the correct soloution! It sounds purely electrical or possibly software to me. I'm going to investigate to try and get as much information as I can, drop the pan and look at the solenoid valves for myself. I did have an issue with my temperature sensor a couple months back. I changed the sensor myself and the issue was gone. taking out the alternator makes me think some sort of unfused direct ground.
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